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picard-tools package

picard-tools 3.0.0+dfsg-1 source package in Ubuntu

Changelog

picard-tools (3.0.0+dfsg-1) unstable; urgency=medium

  * New upstream version 3.0.0+dfsg
  * Refreshing patches
  * Raising Standards version to 4.6.2 (no change)
  * Removing unnecessary versioned B-D
  * Adding nashorn to d/maven.ignoreRules
  * Running the build-time tests from a directory with no '+' in its path
  * Omitting the long-failing jar invocation in the tests

 -- Pierre Gruet <email address hidden>  Tue, 04 Jul 2023 15:23:35 +0200

Upload details

Uploaded by:
Debian Med
Uploaded to:
Sid
Original maintainer:
Debian Med
Architectures:
all
Section:
science
Urgency:
Medium Urgency

See full publishing history Publishing

Series Pocket Published Component Section
Mantic release universe science

Builds

Mantic: [FULLYBUILT] amd64

Downloads

File Size SHA-256 Checksum
picard-tools_3.0.0+dfsg-1.dsc 2.7 KiB 2479ac54677d6d18d7355becf44af39e32d345fc2080672d52a8f90eedcf51fa
picard-tools_3.0.0+dfsg.orig.tar.xz 19.4 MiB c861fb6d98e3cd31bafbf36aa9870469c0404785835e3350c41d043dbae5c467
picard-tools_3.0.0+dfsg-1.debian.tar.xz 22.0 KiB f8af44eb913cf03efb39937b857560ddea2fdcf76b4c19523c8086256fe950a0

Available diffs

No changes file available.

Binary packages built by this source

libpicard-java: Java library to manipulate SAM and BAM files

 SAM (Sequence Alignment/Map) format is a generic format for storing
 large nucleotide sequence alignments. This library provides classes to
 manipulate SAM and BAM files.
 .
 A command line wrapper for this library is provided in the picard-tools
 package.

libpicard-java-doc: Documentation for the java picard library

 SAM (Sequence Alignment/Map) format is a generic format for storing
 large nucleotide sequence alignments. The picard java library provides classes
 to manipulate SAM and BAM files.
 .
 This package contains the javadoc of the picard java library.

picard-tools: Command line tools to manipulate SAM and BAM files

 SAM (Sequence Alignment/Map) format is a generic format for storing
 large nucleotide sequence alignments. Picard Tools includes these
 utilities to manipulate SAM and BAM files:
  AddCommentsToBam FifoBuffer
  AddOrReplaceReadGroups FilterSamReads
  BaitDesigner FilterVcf
  BamIndexStats FixMateInformation
                                    GatherBamFiles
  BedToIntervalList GatherVcfs
  BuildBamIndex GenotypeConcordance
  CalculateHsMetrics IlluminaBasecallsToFastq
  CalculateReadGroupChecksum IlluminaBasecallsToSam
  CheckIlluminaDirectory LiftOverIntervalList
  CheckTerminatorBlock LiftoverVcf
  CleanSam MakeSitesOnlyVcf
  CollectAlignmentSummaryMetrics MarkDuplicates
  CollectBaseDistributionByCycle MarkDuplicatesWithMateCigar
  CollectGcBiasMetrics MarkIlluminaAdapters
  CollectHiSeqXPfFailMetrics MeanQualityByCycle
  CollectIlluminaBasecallingMetrics MergeBamAlignment
  CollectIlluminaLaneMetrics MergeSamFiles
  CollectInsertSizeMetrics MergeVcfs
  CollectJumpingLibraryMetrics NormalizeFasta
  CollectMultipleMetrics PositionBasedDownsampleSam
  CollectOxoGMetrics QualityScoreDistribution
  CollectQualityYieldMetrics RenameSampleInVcf
  CollectRawWgsMetrics ReorderSam
  CollectRnaSeqMetrics ReplaceSamHeader
  CollectRrbsMetrics RevertOriginalBaseQualitiesAndAddMateCigar
  CollectSequencingArtifactMetrics RevertSam
  CollectTargetedPcrMetrics SamFormatConverter
  CollectVariantCallingMetrics SamToFastq
  CollectWgsMetrics ScatterIntervalsByNs
  CompareMetrics SortSam
  CompareSAMs SortVcf
  ConvertSequencingArtifactToOxoG SplitSamByLibrary
  CreateSequenceDictionary SplitVcfs
  DownsampleSam UpdateVcfSequenceDictionary
  EstimateLibraryComplexity ValidateSamFile
  ExtractIlluminaBarcodes VcfFormatConverter
  ExtractSequences VcfToIntervalList
  FastqToSam ViewSam